Japan's criminal justice system is terrible, just terrible.
Crime is very low to start with so police are mostly helpful cop on the corner type or worst case dealing with drunks, gropers, or teen prostitution (but they usually don't bother with that one). There are a very few 'elites' who handle the nasty stuff, and they have an extremely high conviction rate because once they finger you you're going to jail whether you did it or not. Prosecution, defense, and judge all go with that (the detective said so!), so the only thing up for debate, really, is the sentence. There's a grand jury for a few things but they're mostly go along go along too.
And they know nothing at all about technology. There was a thing two (?) years ago where some mother's apartment dwelling otaku freak was cancelling Kurko's Basketball (a popular manga/anime) events left and right for over a year and they couldn't do a damn thing about it. Eventually the freak got so cocky he got careless and did things like using messenger cats. My memory's a little hazy, but it went on seemingly forever and the cops were completely helpless. And they're terrible with corporate crime like this (the handling of the Olympus affair was a disgrace) since usually it's all a matter of what Japanese politicians you have in your pocket - but apparently Mt. Gox didn't have any. Whoops.
I think Karpeles did it, or at least someone close to him at Mt. Gox did it, because it's just entirely too fishy, but I don't think this will prove it.